This research was aimed to assess the distribution of calcium, phosphorus and magnesium within the casein micelles of yak milk. To this aim, nine bulk yak milk samples (Y-milk), collected in three yak farms located in the Chinese province of Qinghai, were compared to nine bulk cow milk samples used as a reference. A quite similar content of colloidal calcium (0.80 vs. 0.77 mmol/g of casein; p > 0.05), a higher content of magnesium (0.05 vs. 0.04 mmol/g of casein; p ≤ 0.01) and a lower content of colloidal phosphorus (0.48 vs. 0.56 mmol/g of casein; p ≤ 0.01) between yak and cow casein micelles were found. Moreover, the yak casein micelles showed a lower value of prosthetic phosphorus (0.20 vs. 0.26 mmol/g of casein; p ≤ 0.05) compared to the cow micelles. The lower values of colloidal and prosthetic phosphorus in yak casein micelles suggest that the yak casein is less phosphorylated than the cow one.